On the transferability of atomic solvation parameters: Ab initio structural prediction of cyclic heptapeptides in DMSO

A statistical mechanics methodology for predicting the solution structures and populations of peptides developed recently is based on a novel method f or optimizing implicit solvation models, which was applied initially to a c yclic hexapeptide in DMSO (C. Baysal and H. Meirovitch, Journal of American Chemical Society, 1998, vol. 120, pp. 800-812). Thus, the molecule has bee n described by the simplified energy function E-tot = E-GRO + Sigma (k)sigm a (k)A(k), where E-GRO is the GROMOS force-field energy, sigma (k) and A(k) are the atomic solvation parameter (ASP) and the solvent accessible surfac e area of atom k, respectively In a more recent study, these ASPs have been found to be transferable to the cyclic pentapeptide cyclo(D-Pro(1)-Ala(2)- Ala(3)-Ala(4)-Ala(5)) in DMSO (C. Baysal and H. Meirovitch, Biopolymers, 20 00, vol. 53, pp. 423-433). In the present paper our methodology is applied to the cyclic heptapeptides axinastatin 2 [cyclo(Asn(1)-Pro(2)-Phe(3)-Val(4 )-Leu(5)-Pro(6)-Val(7))] and axinastatin 3 [cyclo(Asn(1)-Pro(2)-Phe(3)-Ile( 4)-Leu(5)-Pro(6)-Val(7))], in DMSO, which were studied by nmr by Mechnich e t al. (Helvetica Chimica Acta 1997 vol. 80, pp. 1338-1354). The calculation s for axinastatin 2 show that special ASPs should be optimized for the part ially charged side-chain atoms of Asn while the rest of the atoms take thei r values derived in our previous work; this suggests that similar optimizat ion might be needed for other side chains as well. The solution structures of these peptides are obtained ab initio (i.e., without using experimental restraints) by an extensive conformational search based on E-GRO alone and E-tot*, which consists of the new set of ASPs. For E-tot*, the theoretical values of proton-proton distances, (3)J coupling constants, and other prope rties are found to agree very well with the nmr results, and they are alway s better than those based on E-GRO. (C) 2000 John Wiley & Sons, Inc.